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- PDB-7kub: Au1 Domain of VEGF Readthrough Element -

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Basic information

Entry
Database: PDB / ID: 7kub
TitleAu1 Domain of VEGF Readthrough Element
ComponentsRNA (60-MER)
KeywordsRNA / Stop codon readthrough / VEGF mRNA / stem-loop
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / molecular dynamics
Model detailsNMR Structure
AuthorsD'Souza, V.M. / Wagner, N.O. / Edwards, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)55108516 United States
National Science Foundation (NSF, United States)1144152 United States
CitationJournal: To Be Published
Title: Stop codon readthrough in VEGF-A is regulated by complex signals
Authors: Wagner, N.O. / Edwards, J.E. / Abramovich, J. / Gupta, P. / Swaminathan, H. / Rouskin, S. / D'Souza, V.M.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (60-MER)


Theoretical massNumber of molelcules
Total (without water)19,2691
Polymers19,2691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (60-MER)


Mass: 19268.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: GenBank: 163006

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
225isotropic12D 1H-1H NOESY
332isotropic12D 1H-1H NOESY
343isotropic12D 1H-1H NOESY
354isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1100 uM RNA (60-MER), 90% H2O/10% D2OFull_H2O90% H2O/10% D2O
solution2100 uM RNA (60-MER), 100% D2OH3H4_D2O100% D2O
solution3100 uM RNA (60-MER), 100% D2OH2H3_D2O100% D2O
solution4100 uM RNA (60-MER), 100% D2OH1H2_D2O100% D2O
solution5100 uM RNA (60-MER), 100% D2OFull_D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 uMRNA (60-MER)1
100 uMRNA (60-MER)2
100 uMRNA (60-MER)3
100 uMRNA (60-MER)4
100 uMRNA (60-MER)5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMconditions_H2O5.6ambient 280 K
250 mMconditions_D2O_15.6ambient 311 K
350 mMconditions_D2O_28ambient 311 K

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NMR measurement

NMR spectrometerType: Bruker Ascend800 / Manufacturer: Bruker / Model: Ascend800 / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJJohnson, Brucechemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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